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Data from: The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops

Renaut S, Rieseberg LH

Date Published: May 12, 2015

DOI: http://dx.doi.org/10.5061/dryad.8s459

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Title

HA412_trinity_noAltSplice_400bpmin.fa

Description

Link to reference transcriptome described in Renaut et al. 2013 (NatCom), used for all alignments, and previously deposited in Dryad as part of http://dx.doi.org/10.5061/dryad.9q1n4.

Results of PROVEAN analyses identifying deleterious non-synonymous mutations. First column identifies the non-synonymous AA changes and their position (e.g. P113A). The correspondence between this AA change and the SNPs identified in the dataset can be found in this file (new_snp_table_effect). Second column is the Provean score. Third column are the name of the genes.

Results of SIFT analyses identifying deleterious non-synonymous mutations. First column identifies the non-synonymous AA changes and their positions (e.g. S11T). Column 2-6 are the SIFT statistics. Last column are the name of the genes.

Renaut S, Rieseberg LH (2015) The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops. Molecular Biology and Evolution 32(9): 2273-2283. http://dx.doi.org/10.1093/molbev/msv106

Additionally, please cite the Dryad data package:

Renaut S, Rieseberg LH (2015) Data from: The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8s459

AbstractFor populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load of deleterious mutations in 21 accessions from natural populations and 19 domesticated accessions of the common sunflower using whole-transcriptome single nucleotide polymorphism data. Although we find that genetic diversity has been greatly reduced during domestication, the remaining mutations were disproportionally biased toward nonsynonymous substitutions. Bioinformatically predicted deleterious mutations affecting protein function were especially strongly over-represented. We also identify similar patterns in two other domesticated species of the sunflower family (globe artichoke and cardoon), indicating that this phenomenon is not due to idiosyncrasies of sunflower domestication or the sunflower genome. Finally, we provide unequivocal evidence that deleterious mutations accumulate in low recombining regions of the genome, due to the reduced efficacy of purifying selection. These results represent a conundrum for crop improvement efforts. Although the elimination of harmful mutations should be a long-term goal of plant and animal breeding programs, it will be difficult to weed them out because of limited recombination.